Difference between revisions of "Bioinformatics tools"

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==/home/bin==
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''Note: The following are some of my local bioinformatics-related utilities.''
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===Directories===
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*BOINC/
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*[[:Category:Ccp4|CCP4]]/
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*ciftr/
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*[[:Category:EMBOSS|EMBOSS]]/
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*[[make|makefiles]]/
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*mpich2/ (parallel computing)
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*scripts/
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*[[:Category:SEALS|SEALS]]/
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*Sirius/
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*validation/ (validate PDB format files)
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===Utilities===
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*aausage.pl (see: [[Sequence logo]])
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*[[agrep]]
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*[[chcase]] (+v2_chcase.pl)
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*[[ClustalW|clustalw]] / clustalw_help
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*describe
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*dict
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*dotter
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*fa2blc
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*[[gb2tab]]
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*getpdb
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*globin.pep
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*grepseq
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*[[matrix2png]]
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*[[molvolume]]
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*[[naccess]]
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*[[njplot]]
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*pdb2cif.awk / pdb2cif.pl
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*pdbcavity
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*pdbcm / pdbcm.awk
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*pdbinertia
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*pngcrush
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*ps2png.sh
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*[[pymol]]
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*rasmol / rasmol.hlp
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*resize_images
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*rmsfit / rmsfit-fast
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*[[roseplot]]
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*[[shawkle]]
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*[[superpose]] (aka SSM)
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*[[t_coffee]]
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*[[tex2im]]
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*transpose_csv.sh
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*wcseq
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*word_sort_count.pl
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==Multiple Sequence Alignment tools==
 
==Multiple Sequence Alignment tools==
 
*[[Clustalw]]
 
*[[Clustalw]]
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==Other alignment tools==
 
==Other alignment tools==
*[[HMMER]] - [[wp:HMM|HMM]] based alignment
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*[[HMMER]] — [[wikipedia:Hidden Markov model|Hidden Markov model]] based alignment
 
*[[Promoterwise]]
 
*[[Promoterwise]]
 
*[[DBA]]
 
*[[DBA]]
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*[[Genscan]]
 
*[[Genscan]]
 
*[[Genewise]]
 
*[[Genewise]]
 
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*[http://www.cbs.dtu.dk/services/EasyGene/ EasyGene 1.0 Server]
 
* '''Wanted'''
 
* '''Wanted'''
 
** [[SNAP]] (writes [[GFF]] and [[ZFF]]) (this is pretty easy)
 
** [[SNAP]] (writes [[GFF]] and [[ZFF]]) (this is pretty easy)
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==Other tools==
 
==Other tools==
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*[http://meme.sdsc.edu/meme/intro.html MEME/MAST] — motif discovery and search tools
 
*[[Primer3]] - primer predition
 
*[[Primer3]] - primer predition
 
*[[TribeMCL]] - gene family identification
 
*[[TribeMCL]] - gene family identification
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* [[EBI SOAP services]]
 
* [[EBI SOAP services]]
  
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==External links==
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*[http://www.bioperl.org/wiki/Category:Tools BioPerl - Category:Tools]
  
 
[[Category:Bioinformatics| ]]
 
[[Category:Bioinformatics| ]]

Latest revision as of 22:14, 15 May 2008

/home/bin

Note: The following are some of my local bioinformatics-related utilities.

Directories

  • BOINC/
  • CCP4/
  • ciftr/
  • EMBOSS/
  • makefiles/
  • mpich2/ (parallel computing)
  • scripts/
  • SEALS/
  • Sirius/
  • validation/ (validate PDB format files)

Utilities

Multiple Sequence Alignment tools

Whole Genome Multiple Alignment

Pairwise alignment database searches

Other alignment tools

Protein and mRNA to genome (spliced) alignment tools

Gene prediction tools

RNA-related tools

RNA motif prediction tools

RNA secondary structure prediction tools

Sequence family clustering and Orthology prediction

Other tools

Phylogenetics

Reconstruction

Parsimony

Distance

Maximum Likelihood

Bayesian

Molecular Evolution

  • PAML (Codeml, YN00, baseml, evolver)
  • Modeltest supported via Hyphy::Modeltest
  • HyPhy Hyphy::SLAC, Hyphy::REL, Hyphy::FEL

Tree reconciliation

Divergence time estimation

Rates of evolution

Footprinting

Remote and local packages of applications

  • PISE - submit jobs to an external queue with hundreds of bioinformatics applications
  • EMBOSS - run these application locally
  • EBI SOAP services

External links